Citrus Sinensis ID: 030716

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170---
Protein Sequence
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccEEcccccccEEEEEEEEEcccEEEEEEEEEccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccHcccccccccccccccccccccccccccccccccccccccccccHHHHHHccHHHHcccccccccccccccccHHHccEEEEcccccccEEEEEEEEcccEEEEEEEEEcccccccccccEEcccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mlssmalqstvngafttrssfpsqkltvkptkttilhqnrtkpisrnQRLValatpesltaeeatttstetipatpvetkagvsvkqlekpRLVLKFIWMEKNIglaldqsipgygtiplsqyffwprkDAWEELKTTLESKPWISQKMMIILLNQATDIINLWqqsggnltt
Flexible Loop (DISEMBL)
MLSSMALQSTvngafttrssfpsqkltvkptkttilhqnrtkpisrnqrLVALATpesltaeeatttstetipatpvetkagvsvkqleKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Low Complexity Region (SEG)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLValatpesltaeeatttstetipatPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Disordered region (IsUnstruct)
************************************************************************************VKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQ********
Disordered Region (DISOPRED)
*****************************************************************************************KPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLW**S******
Disordered Region (DISEMBL)
**********VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPES************TIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Disordered Region (DISPRO)
*********************************************************SLT**************TPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	173	2.2.26 [Sep-21-2011]
Q9SX22	166	30S ribosomal protein 3-1	yes	no	0.947	0.987	0.620	1e-50
P82412	179	30S ribosomal protein 3,	N/A	no	0.976	0.944	0.533	1e-43
Q9LFV0	183	30S ribosomal protein 3-2	no	no	0.965	0.912	0.494	1e-40
O48609	181	30S ribosomal protein 3,	N/A	no	0.526	0.502	0.747	4e-36
B8HTT7	109	Probable 30S ribosomal pr	yes	no	0.514	0.816	0.547	8e-23
P59327	108	Probable 30S ribosomal pr	yes	no	0.502	0.805	0.534	4e-22
P51351	99	Probable 30S ribosomal pr	N/A	no	0.439	0.767	0.584	1e-21
Q1XDD6	102	Probable 30S ribosomal pr	N/A	no	0.479	0.813	0.558	2e-21
Q9MUN2	123	Probable 30S ribosomal pr	N/A	no	0.433	0.609	0.565	3e-21
Q8YSC1	99	Probable 30S ribosomal pr	yes	no	0.450	0.787	0.556	3e-21

>sp|Q9SX22|RRP31_ARATH 30S ribosomal protein 3-1, chloroplastic OS=Arabidopsis thaliana GN=At1g68590 PE=1 SV=1

 Score =  199 bits (505), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 108/174 (62%), Positives = 127/174 (72%), Gaps = 10/174 (5%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIP 119
           TAE  T T  +T   TP +T     VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIP
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIK--VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIP 111

Query: 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           LS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 112 LSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Probably a ribosomal protein or a ribosome-associated protein.
Arabidopsis thaliana (taxid: 3702)

>sp|P82412|RRP3_SPIOL 30S ribosomal protein 3, chloroplastic OS=Spinacia oleracea GN=PSRP3 PE=1 SV=1

 Score =  175 bits (443), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 95/178 (53%), Positives = 117/178 (65%), Gaps = 9/178 (5%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNR---TKP----ISRNQRLVALATP 56
           SMA+Q  +N A    S + S KL++KP KT      +   + P    + +         P
Sbjct: 3   SMAVQPNIN-AIAKPSIYQSPKLSLKPFKTPAFANPKPFFSSPSFSQLKKKNNWSLFVAP 61

Query: 57  ESLTAEEATTTSTETIPATPV-ETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGY 115
           E+++         +      V + K  V VK ++KPRLVLKFIWMEKNIGLALDQ+IPG+
Sbjct: 62  ETISDVAIMGNEVDIDDDLLVNKEKLKVLVKPMDKPRLVLKFIWMEKNIGLALDQTIPGH 121

Query: 116 GTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           GT+PLS Y+FWPRKDAWEELK  LE+KPWISQK MIILLNQATDIINLWQQSGGNL +
Sbjct: 122 GTVPLSPYYFWPRKDAWEELKVLLENKPWISQKQMIILLNQATDIINLWQQSGGNLAS 179

One of the plastid-specific ribosomal proteins.

Spinacia oleracea (taxid: 3562)

>sp|Q9LFV0|RRP32_ARATH 30S ribosomal protein 3-2, chloroplastic OS=Arabidopsis thaliana GN=At5g15760 PE=2 SV=1

 Score =  165 bits (418), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 91/184 (49%), Positives = 119/184 (64%), Gaps = 17/184 (9%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISR--------NQRLV----A 52
           MA+Q+  + +F  R++ PSQKL+ KP     L   + KP SR        NQ  +    +
Sbjct: 1   MAVQANQSASFGFRTASPSQKLSSKPIAHISL-STKLKPSSRPSLSCSTWNQGQIPARHS 59

Query: 53  LATPESLTAEEATTTSTETIPAT---PV-ETKAGVSVKQLEKPRLVLKFIWMEKNIGLAL 108
              P       +  T +  +P +   P+ + K  V VK LEKP++VLKF+WM+K+IG+AL
Sbjct: 60  CINPGIFAYPPSNLTFSHELPESESPPLGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVAL 119

Query: 109 DQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSG 168
           D  IPG+GTIPLS Y+FWPRKDAWEELKT LESKPWIS+   + LLNQATDIINLWQ SG
Sbjct: 120 DHMIPGFGTIPLSPYYFWPRKDAWEELKTLLESKPWISELHRVFLLNQATDIINLWQSSG 179

Query: 169 GNLT 172
           G+L+
Sbjct: 180 GDLS 183

Probably a ribosomal protein or a ribosome-associated protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O48609|RRP3_HORVU 30S ribosomal protein 3, chloroplastic OS=Hordeum vulgare GN=PSRP3 PE=2 SV=1

 Score =  150 bits (379), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 68/91 (74%), Positives = 77/91 (84%)

Query: 83  VSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESK 142
           V V + + P LVLKFIWMEKNIG+ALDQ +PG G+IPLS Y+FWPRKDAWEEL+  LE K
Sbjct: 91  VEVPEKQDPMLVLKFIWMEKNIGIALDQMVPGVGSIPLSPYYFWPRKDAWEELRAKLEEK 150

Query: 143 PWISQKMMIILLNQATDIINLWQQSGGNLTT 173
            WISQK MIILLNQATDIINLWQQ GG+L+T
Sbjct: 151 EWISQKQMIILLNQATDIINLWQQGGGSLST 181

Probably a ribosomal protein or a ribosome-associated protein.

Hordeum vulgare (taxid: 4513)

>sp|B8HTT7|RRP3_CYAP4 Probable 30S ribosomal protein PSRP-3 OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=Cyan7425_0465 PE=3 SV=1

 Score =  106 bits (264), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/95 (54%), Positives = 66/95 (69%), Gaps = 6/95 (6%)

Query: 76  PVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEEL 135
           PV+T   VS+ Q      +LK +W++ N+ LA+DQ + G GT PL+ YFFWPR DAWE+L
Sbjct: 2   PVQTILEVSLSQF-----ILKVLWLDSNVALAVDQVV-GKGTSPLTSYFFWPRADAWEQL 55

Query: 136 KTTLESKPWISQKMMIILLNQATDIINLWQQSGGN 170
           KT LE K WIS+   I LLN+ATDIIN WQ+ G N
Sbjct: 56  KTELEKKTWISEADRIALLNRATDIINYWQEEGRN 90

Probably a ribosomal protein or a ribosome-associated protein.

Cyanothece sp. (strain PCC 7425 / ATCC 29141) (taxid: 395961)

>sp|P59327|RRP3_THEEB Probable 30S ribosomal protein PSRP-3 OS=Thermosynechococcus elongatus (strain BP-1) GN=tlr0301 PE=3 SV=1

 Score =  104 bits (259), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 47/88 (53%), Positives = 63/88 (71%), Gaps = 1/88 (1%)

Query: 83  VSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESK 142
           +S ++LE  R  L+ +W+EK++ +A+DQ I G GT PL+ YFFWPR DAWE LK  LE K
Sbjct: 3   ISFRRLELSRFTLRVLWLEKDVAIAVDQ-IVGKGTSPLTSYFFWPRTDAWELLKAELEKK 61

Query: 143 PWISQKMMIILLNQATDIINLWQQSGGN 170
            WI++   I LLN+AT+IIN WQ+ G N
Sbjct: 62  SWITEAERIELLNRATEIINYWQEEGKN 89

Probably a ribosomal protein or a ribosome-associated protein.

Thermosynechococcus elongatus (strain BP-1) (taxid: 197221)

>sp|P51351|RRP3_PORPU Probable 30S ribosomal protein 3, chloroplastic OS=Porphyra purpurea GN=ycf65 PE=3 SV=1

 Score =  102 bits (254), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 92  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 151
           +  LK +W+E NI +A+DQ I G GT PL+ YFFWPR DAWEELK  LESKPWI+++  I
Sbjct: 3   KFTLKVLWLENNIAIAIDQ-IVGNGTSPLTSYFFWPRNDAWEELKAELESKPWIAERDRI 61

Query: 152 ILLNQATDIINLWQQSG 168
            LLN+ T++IN WQ+ G
Sbjct: 62  ELLNKTTEVINYWQEEG 78

Probably a ribosomal protein or a ribosome-associated protein.

Porphyra purpurea (taxid: 2787)

>sp|Q1XDD6|RRP3_PORYE Probable 30S ribosomal protein 3, chloroplastic OS=Porphyra yezoensis GN=ycf65 PE=3 SV=1

 Score =  102 bits (253), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 62/86 (72%), Gaps = 3/86 (3%)

Query: 83  VSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESK 142
           + +K L K    LK +W+E NI +A+DQ I G GT PL+ YFFWPR DAWEELK  LESK
Sbjct: 1   MEIKNLSK--FTLKVLWLENNIAIAIDQ-IVGNGTSPLTSYFFWPRNDAWEELKAELESK 57

Query: 143 PWISQKMMIILLNQATDIINLWQQSG 168
           PWI+++  I LLN+ T++IN WQ+ G
Sbjct: 58  PWIAERDRIELLNKTTEVINYWQEEG 83

Probably a ribosomal protein or a ribosome-associated protein.

Porphyra yezoensis (taxid: 2788)

>sp|Q9MUN2|RRP3_MESVI Probable 30S ribosomal protein 3, chloroplastic OS=Mesostigma viride GN=ycf65 PE=3 SV=1

 Score =  101 bits (251), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 92  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 151
           + VLKF+W+EKN+ + +DQ +   G  P+++YFFWPRKDAWEELK  L +KPWIS    I
Sbjct: 20  KFVLKFLWLEKNLAVTVDQ-VTNRGNSPITEYFFWPRKDAWEELKDALANKPWISYDESI 78

Query: 152 ILLNQATDIINLWQQS 167
            LLNQ TD+IN WQ+ 
Sbjct: 79  ALLNQTTDVINYWQED 94

Probably a ribosomal protein or a ribosome-associated protein.

Mesostigma viride (taxid: 41882)

>sp|Q8YSC1|RRP3_NOSS1 Probable 30S ribosomal protein PSRP-3 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=asr3168 PE=3 SV=2

 Score =  101 bits (251), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 60/79 (75%), Gaps = 1/79 (1%)

Query: 92  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 151
           + +LK +W+++N+ LA+DQ + G GT PL++YFFWPR DAWEELK  LESK WIS    +
Sbjct: 3   KFILKILWLDENVALAVDQVV-GKGTSPLTKYFFWPRNDAWEELKKELESKHWISDLDRV 61

Query: 152 ILLNQATDIINLWQQSGGN 170
            LLN+AT++IN WQ+ G N
Sbjct: 62  ELLNKATEVINYWQEEGRN 80

Probably a ribosomal protein or a ribosome-associated protein.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	173
255576477	180	Plastid-specific 30S ribosomal protein 3	0.965	0.927	0.631	5e-54
224111708	189	predicted protein [Populus trichocarpa]	0.971	0.888	0.617	2e-52
224099355	189	predicted protein [Populus trichocarpa]	0.965	0.883	0.609	7e-52
21554275	166	plastid-specific ribosomal protein 3 pre	0.947	0.987	0.620	3e-49
145326692	163	30S ribosomal protein 3-1 [Arabidopsis t	0.930	0.987	0.614	3e-49
18409071	166	30S ribosomal protein 3-1 [Arabidopsis t	0.947	0.987	0.620	4e-49
225452011	176	PREDICTED: 30S ribosomal protein 3, chlo	0.976	0.960	0.569	3e-47
296087288	175	unnamed protein product [Vitis vinifera]	0.959	0.948	0.573	1e-46
297841583	162	plastid-specific ribosomal protein 3 pre	0.861	0.919	0.655	4e-46
147784271	179	hypothetical protein VITISV_004015 [Viti	0.907	0.877	0.575	2e-45

>gi|255576477|ref|XP_002529130.1| Plastid-specific 30S ribosomal protein 3, chloroplast precursor, putative [Ricinus communis] gi|223531409|gb|EEF33243.1| Plastid-specific 30S ribosomal protein 3, chloroplast precursor, putative [Ricinus communis]

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 115/182 (63%), Positives = 132/182 (72%), Gaps = 15/182 (8%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTILH-------------QNRTKPISRNQRLV 51
           MA+QS V+ +  T S  P +    K  KT+I                 + +PISRN+RL 
Sbjct: 1   MAIQSGVS-SILTYSPVPHRTPFCKSIKTSIFANPKISLLYSSTILDPKMRPISRNERLT 59

Query: 52  ALATPESLTAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQS 111
             A+PE+LT E+ T+ + E I    +E K  V+VKQ+EKPRLVLKFIWMEKNIGLALDQ 
Sbjct: 60  TFASPEALTVEDKTSETEEPISDDIIE-KVEVAVKQVEKPRLVLKFIWMEKNIGLALDQV 118

Query: 112 IPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNL 171
           IPG+GTIPLS YFFWPRKDAWEELKTTLESKPWISQK MIILLNQATDIINLWQQSGGNL
Sbjct: 119 IPGHGTIPLSPYFFWPRKDAWEELKTTLESKPWISQKKMIILLNQATDIINLWQQSGGNL 178

Query: 172 TT 173
           TT
Sbjct: 179 TT 180

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111708|ref|XP_002315948.1| predicted protein [Populus trichocarpa] gi|222864988|gb|EEF02119.1| predicted protein [Populus trichocarpa]

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 116/188 (61%), Positives = 130/188 (69%), Gaps = 20/188 (10%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTT--------ILH-----QNRTKPISRNQRL 50
           S+A Q   +  FT  SS P Q  + K  K T        ++H       + K +SRNQR 
Sbjct: 3   SVAFQCGFSNVFTN-SSLPCQTPSCKTFKATFSTNPKPNLIHSSTFLDRKRKRVSRNQRY 61

Query: 51  VALATPESLTAE-----EATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIG 105
              A PE+LT E       +T + E+IPA   E KA V VKQ+EKPRLVLKFIWMEKNIG
Sbjct: 62  TTFAAPEALTVETPIDTPPSTETEESIPAQGTE-KAEVLVKQVEKPRLVLKFIWMEKNIG 120

Query: 106 LALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQ 165
           LALDQ IPG+GT+PLS YFFWPRKDAWEELK TLESKPWISQK MIILLNQATDIINLWQ
Sbjct: 121 LALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQATDIINLWQ 180

Query: 166 QSGGNLTT 173
           QSGGNLTT
Sbjct: 181 QSGGNLTT 188

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099355|ref|XP_002311451.1| predicted protein [Populus trichocarpa] gi|222851271|gb|EEE88818.1| predicted protein [Populus trichocarpa]

 Score =  208 bits (529), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 114/187 (60%), Positives = 126/187 (67%), Gaps = 20/187 (10%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPI-------------SRNQRL 50
           SMA QS VN  FT  S  P +  + K  K TI    +  PI             SRNQR 
Sbjct: 3   SMAFQSGVNNVFTYYS-LPCRTPSCKTFKATISVNPKPNPIRSSTFFDRERRHVSRNQRY 61

Query: 51  VALATPESLTAE-----EATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIG 105
              A PE+L AE       +  + E+IP    E KA + VKQ+EKPRLVLKF+WMEKNIG
Sbjct: 62  TTFAVPEALAAETPADAPPSNAAGESIPIQETE-KAELVVKQVEKPRLVLKFVWMEKNIG 120

Query: 106 LALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQ 165
           LALDQ IPG+GT+PLS YFFWPRKDAWEELK TLESKPWISQK MIILLNQATDIINLWQ
Sbjct: 121 LALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQATDIINLWQ 180

Query: 166 QSGGNLT 172
           QSGGNLT
Sbjct: 181 QSGGNLT 187

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21554275|gb|AAM63350.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis thaliana]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 108/174 (62%), Positives = 127/174 (72%), Gaps = 10/174 (5%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIP 119
           TAE  T T  +T   TP +T     VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIP
Sbjct: 56  TAE--TVTGIDTSDNTPQQTTK--VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIP 111

Query: 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           LS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 112 LSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145326692|ref|NP_001077793.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana] gi|332196696|gb|AEE34817.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/174 (61%), Positives = 127/174 (72%), Gaps = 13/174 (7%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIP 119
           TAE  T T  +T   TP +T     +K  EK R+VLKF+WMEKNIGL LDQ +PG+GTIP
Sbjct: 56  TAE--TVTGIDTSDNTPQQT-----IKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIP 108

Query: 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           LS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 109 LSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 162

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18409071|ref|NP_564934.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana] gi|28380141|sp|Q9SX22.1|RRP31_ARATH RecName: Full=30S ribosomal protein 3-1, chloroplastic; AltName: Full=Plastid-specific 30S ribosomal protein 3-1; Short=PSRP-3 1; Flags: Precursor gi|5734719|gb|AAD49984.1|AC008075_17 ESTs gb|H37416, gb|T21163, gb|T76138 and gb|AA651329 come from this gene [Arabidopsis thaliana] gi|28393198|gb|AAO42029.1| unknown protein [Arabidopsis thaliana] gi|28827558|gb|AAO50623.1| unknown protein [Arabidopsis thaliana] gi|332196695|gb|AEE34816.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana]

 Score =  199 bits (505), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 108/174 (62%), Positives = 127/174 (72%), Gaps = 10/174 (5%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIP 119
           TAE  T T  +T   TP +T     VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIP
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIK--VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIP 111

Query: 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           LS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 112 LSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452011|ref|XP_002283616.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like isoform 1 [Vitis vinifera] gi|359488272|ref|XP_003633730.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like isoform 2 [Vitis vinifera]

 Score =  192 bits (489), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 102/179 (56%), Positives = 126/179 (70%), Gaps = 10/179 (5%)

Query: 1   MLSSMALQSTVNGAFTTRSSFP-----SQKLTVKPTKTTILHQNRTKPISRNQRLVALAT 55
           M+ SMA+Q   N A  + + FP     + +L  K +    L+  R+   S N RL A   
Sbjct: 1   MMLSMAVQPNPNAALKSYT-FPMSSNRNHRLMFKSSNALSLYSTRSA--STNLRLRASPA 57

Query: 56  PE-SLTAEEATTTSTETIPATPVET-KAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIP 113
           P  ++   E ++   E++ A+P++  K GV VK +EKPRLVLKFIWMEKNIG+ALDQ+IP
Sbjct: 58  PVVAVAVSEQSSAPQESLSASPLDVEKLGVVVKPMEKPRLVLKFIWMEKNIGVALDQAIP 117

Query: 114 GYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLT 172
           G+GTIPLS Y+FWPRKDAWEE+K  LESKPWISQK MIILLNQATDIINLWQQSGGNL 
Sbjct: 118 GHGTIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIINLWQQSGGNLA 176

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087288|emb|CBI33662.3| unnamed protein product [Vitis vinifera]

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 101/176 (57%), Positives = 124/176 (70%), Gaps = 10/176 (5%)

Query: 4   SMALQSTVNGAFTTRSSFP-----SQKLTVKPTKTTILHQNRTKPISRNQRLVALATPE- 57
           SMA+Q   N A  + + FP     + +L  K +    L+  R+   S N RL A   P  
Sbjct: 3   SMAVQPNPNAALKSYT-FPMSSNRNHRLMFKSSNALSLYSTRSA--STNLRLRASPAPVV 59

Query: 58  SLTAEEATTTSTETIPATPVET-KAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYG 116
           ++   E ++   E++ A+P++  K GV VK +EKPRLVLKFIWMEKNIG+ALDQ+IPG+G
Sbjct: 60  AVAVSEQSSAPQESLSASPLDVEKLGVVVKPMEKPRLVLKFIWMEKNIGVALDQAIPGHG 119

Query: 117 TIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLT 172
           TIPLS Y+FWPRKDAWEE+K  LESKPWISQK MIILLNQATDIINLWQQSGGNL 
Sbjct: 120 TIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIINLWQQSGGNLA 175

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297841583|ref|XP_002888673.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis lyrata subsp. lyrata] gi|297334514|gb|EFH64932.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis lyrata subsp. lyrata]

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 101/154 (65%), Positives = 118/154 (76%), Gaps = 5/154 (3%)

Query: 21  FPSQKLTVKPTKTTILHQNRT-KPISRNQRLVALATPESLTAEEATTTSTETIPATPVET 79
           F SQ   +  T +T L  N+T KPIS  ++++ LA PE+LTAE  T T  +T   TP +T
Sbjct: 12  FISQHPKLSITASTPLFLNQTTKPISVKRKIITLAAPETLTAE--TVTGIDTSDNTPQQT 69

Query: 80  KAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTL 139
                VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIPLS YFFWPRKDAWEELK+TL
Sbjct: 70  TK--VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIPLSPYFFWPRKDAWEELKSTL 127

Query: 140 ESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
           E+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 128 EAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 161

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784271|emb|CAN68341.1| hypothetical protein VITISV_004015 [Vitis vinifera]

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 107/186 (57%), Positives = 122/186 (65%), Gaps = 29/186 (15%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTI--------LHQN--------RTKPISRNQ 48
           MA QS++N  F   SSFPSQ  + K +KT          L Q         RTKP  + Q
Sbjct: 1   MAAQSSINSTFIC-SSFPSQNPSFKISKTPFPIPLNPKPLFQRSSTXTPGIRTKPSMKLQ 59

Query: 49  RLVALATPESLTAEEATTTSTETIPATPVET----KAGVSVKQLEKPRLVLKFIWMEKNI 104
           RL   A  E+ TAE +T        A P+ +    K  V VK +E PRLVLKF+WMEKNI
Sbjct: 60  RLAVSAASEARTAEPST--------ANPISSEENEKVEVIVKVMETPRLVLKFVWMEKNI 111

Query: 105 GLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLW 164
           G+ALDQ IPGYGT PLS Y+FWP KDAWEELK+TLESKPWISQK MIILLN+ATDIINLW
Sbjct: 112 GVALDQVIPGYGTNPLSPYYFWPGKDAWEELKSTLESKPWISQKKMIILLNEATDIINLW 171

Query: 165 QQSGGN 170
           QQSGGN
Sbjct: 172 QQSGGN 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	173
TAIR|locus:2026940	166	PSRP3/1 "plastid-specifi	0.947	0.987	0.551	2.5e-42
TAIR|locus:2143211	183	PSRP3/2 "plastid-specifi	0.537	0.508	0.731	3.6e-40

TAIR|locus:2026940 PSRP3/1 "plastid-specific ribosomal protein 3/1" [Arabidopsis thaliana (taxid:3702)]

 Score = 448 (162.8 bits), Expect = 2.5e-42, P = 2.5e-42
 Identities = 96/174 (55%), Positives = 113/174 (64%)

Query:     1 MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVXXXXXXXX 59
             M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++        
Sbjct:     1 MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query:    60 XXXXXXXXXXXXXXXXPVETKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIP 119
                             P +T     VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIP
Sbjct:    56 TAETVTGIDTSDNT--PQQTIK--VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIP 111

Query:   120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 173
             LS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct:   112 LSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0032544 "plastid translation" evidence=IMP

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

TAIR|locus:2143211 PSRP3/2 "plastid-specific ribosomal protein 3/2" [Arabidopsis thaliana (taxid:3702)]

 Score = 377 (137.8 bits), Expect = 3.6e-40, Sum P(2) = 3.6e-40
 Identities = 68/93 (73%), Positives = 80/93 (86%)

Query:    80 KAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTL 139
             K  V VK LEKP++VLKF+WM+K+IG+ALD  IPG+GTIPLS Y+FWPRKDAWEELKT L
Sbjct:    91 KMRVLVKPLEKPKVVLKFVWMQKDIGVALDHMIPGFGTIPLSPYYFWPRKDAWEELKTLL 150

Query:   140 ESKPWISQKMMIILLNQATDIINLWQQSGGNLT 172
             ESKPWIS+   + LLNQATDIINLWQ SGG+L+
Sbjct:   151 ESKPWISELHRVFLLNQATDIINLWQSSGGDLS 183

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0009536 "plastid" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SX22	RRP31_ARATH	No assigned EC number	0.6206	0.9479	0.9879	yes	no
P82412	RRP3_SPIOL	No assigned EC number	0.5337	0.9768	0.9441	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT1G68590	plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative; plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative; FUNCTIONS IN- structural constituent of ribosome; INVOLVED IN- translation; LOCATED IN- thylakoid, chloroplast thylakoid membrane, chloroplast; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Ribosomal protein, PSRP-3/Ycf65 (InterPro-IPR006924); BEST Arabidopsis thaliana protein match is- plastid-specific 30S ribosomal protein 3, putative / PSRP-3, putative (TAIR-AT5G15760.1); Has 334 Blast hits [...] (166 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	PPL1	PPL1 (PsbP-like protein 1); calcium ion binding; PsbP-like protein 1 (PPL1); FUNCTIONS IN- calc [...] (230 aa)			•	•					0.944
	PSB28	PSB28 (PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN); Similar to PsbW subunit of photosystem II [...] (183 aa)			•	•					0.944
	AT5G52970	thylakoid lumen 15.0 kDa protein; thylakoid lumen 15.0 kDa protein; FUNCTIONS IN- molecular_fun [...] (223 aa)			•	•					0.926
	emb2184	emb2184 (embryo defective 2184); structural constituent of ribosome; embryo defective 2184 (emb [...] (144 aa)			•	•					0.926
	AT1G14345	oxidoreductase; oxidoreductase; FUNCTIONS IN- oxidoreductase activity; INVOLVED IN- oxidation r [...] (196 aa)			•	•					0.925
	CYP38	CYP38 (cyclophilin 38); peptidyl-prolyl cis-trans isomerase; Encodes a chloroplast cyclophilin [...] (437 aa)			•	•					0.924
	PSAL	PSAL (photosystem I subunit L); Encodes subunit L of photosystem I reaction center. (219 aa)			•	•					0.920
	PSBO2	PSBO2 (PHOTOSYSTEM II SUBUNIT O-2); oxygen evolving/ poly(U) binding; Encodes a protein which i [...] (331 aa)			•	•					0.920
	AT1G50900	unknown protein; FUNCTIONS IN- molecular_function unknown; INVOLVED IN- biological_process unkn [...] (175 aa)				•					0.917
	LIL3:1	LIL3-1; transcription factor; Encodes Lil3-1 (light-harvesting-like) protein. Belongs to the Lh [...] (262 aa)				•					0.917

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	173
CHL00163	99	CHL00163, ycf65, putative ribosomal protein 3; Val	3e-33
PRK02724	104	PRK02724, PRK02724, hypothetical protein; Provisio	3e-31
pfam04839	47	pfam04839, PSRP-3_Ycf65, Plastid and cyanobacteria	1e-23

>gnl|CDD|214381 CHL00163, ycf65, putative ribosomal protein 3; Validated

 Score =  113 bits (284), Expect = 3e-33
 Identities = 44/81 (54%), Positives = 57/81 (70%), Gaps = 1/81 (1%)

Query: 91  PRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMM 150
            +  LK +W+E NIG+A+DQ + G GT PL+ YFFWPR DAWE LK  LESKPWIS+   
Sbjct: 2   QKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDER 60

Query: 151 IILLNQATDIINLWQQSGGNL 171
           I +LN+ T+IIN WQ++    
Sbjct: 61  IEILNKTTEIINYWQENKKKY 81

Length = 99

>gnl|CDD|235062 PRK02724, PRK02724, hypothetical protein; Provisional

 Score =  108 bits (271), Expect = 3e-31
 Identities = 43/84 (51%), Positives = 62/84 (73%), Gaps = 1/84 (1%)

Query: 87  QLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWIS 146
           + ++ R +LK +W++ N+ LA+DQ I G GT PL+ YFFWPR DAWE+LKT LESK WI+
Sbjct: 3   KADEGRFILKVLWLDDNVALAVDQ-IVGKGTSPLTAYFFWPRNDAWEQLKTELESKHWIT 61

Query: 147 QKMMIILLNQATDIINLWQQSGGN 170
           +   + +LN+AT++IN WQ+ G  
Sbjct: 62  ENERVEVLNKATEVINYWQEEGKG 85

Length = 104

>gnl|CDD|203104 pfam04839, PSRP-3_Ycf65, Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)

 Score = 87.4 bits (217), Expect = 1e-23
 Identities = 32/47 (68%), Positives = 39/47 (82%)

Query: 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQ 166
           L++YFFWPR DAWE+LK  LESKPWIS+   + LLNQAT+IIN WQ+
Sbjct: 1   LTEYFFWPRTDAWEQLKAELESKPWISEAERVNLLNQATEIINYWQE 47

This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA. Length = 47

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	173
PRK02724	104	hypothetical protein; Provisional	100.0
CHL00163	99	ycf65 putative ribosomal protein 3; Validated	100.0
PF04839	49	PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal	99.98

>PRK02724 hypothetical protein; Provisional

Probab=100.00  E-value=4.6e-50  Score=306.57  Aligned_cols=83  Identities=51%  Similarity=1.037  Sum_probs=79.9

Q ss_pred             CCCCcEEEEEEeecCceeEEeeeeecCCCCccCcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716           88 LEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS  167 (173)
Q Consensus        88 ~~~~rfvLK~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~  167 (173)
                      .+++||+||||||||||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+|||++||||||||++
T Consensus         4 ~~~~rfvlKvlWle~~iaiAvDQ~v-g~~t~PLT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~WQe~   82 (104)
T PRK02724          4 ADEGRFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRNDAWEQLKTELESKHWITENERVEVLNKATEVINYWQEE   82 (104)
T ss_pred             cccceEEEEEEEeccceeEEeeeec-CCCCCcCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence            4679999999999999999999999 999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 030716          168 GGNL  171 (173)
Q Consensus       168 ~~~~  171 (173)
                      |++-
T Consensus        83 ~~~~   86 (104)
T PRK02724         83 GKGK   86 (104)
T ss_pred             cCCC
Confidence            7653

>CHL00163 ycf65 putative ribosomal protein 3; Validated

Probab=100.00  E-value=5.8e-50  Score=303.79  Aligned_cols=80  Identities=55%  Similarity=1.063  Sum_probs=77.6

Q ss_pred             CCcEEEEEEeecCceeEEeeeeecCCCCccCcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhcCC
Q 030716           90 KPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGG  169 (173)
Q Consensus        90 ~~rfvLK~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~~~  169 (173)
                      ++||+|||||||++|||||||+| |+|++|||+||||||+||||+||.+||+||||+++|||+||||+|||||||||+++
T Consensus         1 m~kf~lKvlWl~~~iaiAvDq~v-~~~t~PlT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~Wqe~~~   79 (99)
T CHL00163          1 MQKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDERIEILNKTTEIINYWQENKK   79 (99)
T ss_pred             CCeEEEEEEEecCceEEEEeeee-CCCCccCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHccC
Confidence            58999999999999999999999 88999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 030716          170 N  170 (173)
Q Consensus       170 ~  170 (173)
                      +
T Consensus        80 ~   80 (99)
T CHL00163         80 K   80 (99)
T ss_pred             C
Confidence            5

>PF04839 PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65); InterPro: IPR006924 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.98  E-value=1.7e-33  Score=191.53  Aligned_cols=48  Identities=71%  Similarity=1.297  Sum_probs=41.8

Q ss_pred             CcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716          120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS  167 (173)
Q Consensus       120 LT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~  167 (173)
                      ||+||||||+||||+||.+||+|+||+++|||.|||++||||||||++
T Consensus         1 lT~yfFWPr~DAWe~lk~eLe~K~WIs~~e~i~lLN~~TeiIN~Wqe~   48 (49)
T PF04839_consen    1 LTEYFFWPREDAWEQLKNELESKPWISEKERIELLNQATEIINYWQEE   48 (49)
T ss_dssp             -S--EEETTS-HHHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCCcccCCCCcHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            799999999999999999999999999999999999999999999996

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome, 0009536 plastid; PDB: 2KT9_A.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	173
2kt9_A	116	Solution Nmr Structure Of Probable 30s Ribosomal Pr		8e-20

>pdb|2KT9|A Chain A, Solution Nmr Structure Of Probable 30s Ribosomal Protein Psrp-3 (Ycf65-Like Protein) From Synechocystis Sp. (Strain Pcc 6803), Northeast Structural Genomics Consortium Target Target Sgr46 Length = 116

Iteration: 1
 Score = 92.8 bits (229), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 56/73 (76%), Gaps = 1/73 (1%)
Query: 93  LVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMII 152
            +LK +W+++N+ +A+DQ I G GT PL+ YFFWPR DAW++LK  LE+K WI++   I 
Sbjct: 10  FILKVLWLDQNVAIAVDQ-IVGKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRIN 68
Query: 153 LLNQATDIINLWQ 165
           +LNQAT++IN WQ
Sbjct: 69  VLNQATEVINFWQ 81
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	173
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	3e-41

>2kt9_A Probable 30S ribosomal protein PSRP-3; structural genomics, northeast structural genomics consortium (NESG), target SGR46, PSI-2; NMR {Synechocystis SP} Length = 116

 Score =  133 bits (336), Expect = 3e-41
 Identities = 38/82 (46%), Positives = 56/82 (68%), Gaps = 1/82 (1%)

Query: 86  KQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWI 145
                   +LK +W+++N+ +A+DQ + G GT PL+ YFFWPR DAW++LK  LE+K WI
Sbjct: 3   ASTVHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWI 61

Query: 146 SQKMMIILLNQATDIINLWQQS 167
           ++   I +LNQAT++IN WQ  
Sbjct: 62  AEADRINVLNQATEVINFWQDL 83

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	173
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	100.0

>2kt9_A Probable 30S ribosomal protein PSRP-3; structural genomics, northeast structural genomics consortium (NESG), target SGR46, PSI-2; NMR {Synechocystis SP}

Probab=100.00  E-value=7e-49  Score=303.47  Aligned_cols=77  Identities=49%  Similarity=1.044  Sum_probs=75.6

Q ss_pred             CCCcEEEEEEeecCceeEEeeeeecCCCCccCcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHh
Q 030716           89 EKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQ  166 (173)
Q Consensus        89 ~~~rfvLK~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe  166 (173)
                      -++||+|||||||+||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+||||+|||||||||
T Consensus         6 ~m~rf~LKvlWlek~IaiAvDQ~v-g~~t~PLT~YfFWPr~DAWe~LK~eLEsK~WIse~e~i~lLN~~TeiIN~WQe   82 (116)
T 2kt9_A            6 VHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRINVLNQATEVINFWQD   82 (116)
T ss_dssp             CCCCEEEEEEECSSCEEEEEEEEE-TTEEEECSCCEEETTSCHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhheeeEEEeccceeEEeeeee-cCCCCCCcceeeCCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999 99999999999999999999999999999999999999999999999999998

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

No hit with probability above 80.00